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Description
Flashcards by Dominique M, updated more than 1 year ago
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Created by Dominique M
almost 6 years ago
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| Question | Answer |
| What is the consequence of a block at the start of the citric acid cycle knowing that involved proteins have strong epistatic interactions? | The proteins in such a cycle work in coordinated fashion (optimized clusters). A block at the start has severe consequences for the function of the cycle. |
| Explain the relationship between 'linear dependence' and 'the ribosome' | There is need for co-regulation as there should be balance between the production of subunits (there is a strong epistatic interaction) |
| Argue why it can be complicated to find a certain protein. | Proteins have different life times, localization and concentration in the cell. The protein of interest may have a short life time and is degraded rapidly. |
| What makes detection of all proteins at the same time difficult? | The proteins are present in an extremely wide range of concentrations. They cannot be captured with the same machine settings. |
| What are techniques to determine protein structure? | X-ray crystallography, NMR, single-particle EM, homology modelling |
| What is the principle of X-ray crystallography? | X-ray beams hit a molecule after which a diffraction pattern is generated. This gives information about the protein structure by means of an electron density map. |
| What is the principle of NMR? What is a benefit? | A chemical shift of the H-atoms in a molecule is induced and measured. A benefit is that movements of the molecule can be captured. |
| What is the principle of single particle EM? | Proteins are hit with a beam resulting in a diffraction pattern. Many diffraction patterns are bundled to generate the protein structure. |
| Which two MS techniques are most used? | ESI-MS and MALDI-TOF |
| What is the principle of ESI-MS? | Charged particles are selected on charge. Prediction occurs with TOF - time of flight is directly related to the size of a molecule. |
| What is the principle of MALDI-TOF? | A laser beam is used to release molecules from a solid state. This generates fragments. These are selected on charge and mass. |
| What is the difference is mass of various isotopes? | 1 Dalton |
| Can a protein be identified based on its mass only? What is the solution? | No, not all proteins have different masses. Proteins are fragmented into peptides and as sequences differ, breaking points do as well. |
| Name the steps for protein identification with mass spectrometry. | Proteins --> separation (HPLC) --> digestion (trypsin) --> ioniser --> selection of double-charged ions --> selected fragmented (collision-induced decay) --> singly charged daughter ions analyzed |
| Why are double charged peptides preferred? | When the peptide breaks, the two daughter peptides will have a single charge (while if charge = 1 only one daughter ion will be charged). |
| What is the name of the ions generated when a peptide is broken at its peptide bond? | b-ions and y-ions. |
| Name the use of the quadrupole mass analyzer. | Four electrodes park molecules. Only molecules with a certain m/z are flown through while other ones are attached to the electrodes (+ or -). |
| We end up with b-ions and y-ions. What do the 'b' and 'y' part refer to? | After breakage: b stands for the part BEFORE the peptide bond. Y stands for the part AFTER the peptide bond. |
| What do the numbers indicate in the following situation? b2, y2 | The numbers indicate the amount of amino acids. |
| Peptide identification is difficult. Name an approach other than de novo identification. | Make in silico database (need a well-annotated genome for this) --> predict all b and y fragments (knowing the cut sites) Now let the computer compare fragments to the database --> identification. |
| You have a sample with 6000 proteins which vary in copy number. Which technique is appropriate? | Use LC-MS to separate and simplify the spectrum. |
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